ComplexViewer: visualization of curated macromolecular complexes

Abstract

Summary: Proteins frequently function as parts of complexes, assemblages of multiple proteins and other biomolecules, yet network visualizations usually only show proteins as parts of binary interactions. ComplexViewer visualizes interactions with more than two participants and thereby avoids the need to first expand these into multiple binary interactions. Furthermore, if binding regions between molecules are known then these can be displayed in the context of the larger complex.

Availability and implementation: freely available under Apache version 2 license; EMBL-EBI Complex Portal: http://www.ebi.ac.uk/complexportal; Source code: https://github.com/MICommunity/ComplexViewer; Package: https://www.npmjs.com/package/complexviewer; http://biojs.io/d/complexviewer. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js.

Contact: colin.combe@ed.ac.uk or juri.rappsilber@ed.ac.uk.

Fig. 1

(i) EBI-9691559: Mitochondrial pyruvate dehydrogenase complex. The complex (in blue) is a single n-ary interaction in which interactions between certain participants are known and some binding sites are known. Stoichiometry information is given in square brackets. (ii) EBI-9008420: Haemoglobin HbA complex. This complex is shown both with the stoichiometry information collapsed (left) and expanded (right)